[gmx-users] "coarse_grain.tcl" script does not show all of the coarse-grained bonds in vmd

Ozge Engin ozge.engin at gmail.com
Thu Dec 3 10:23:46 CET 2009

Hi all,

I was trying to show the bonds between my CG beads in VMD. I have four CG
beads per each molecule, and there are 18 separate molecules which contain
these four beads, which results in having 72 CG beads in total. Therefore,
I  expect  to see  54 CG bonds in the end.

I used the "coarse_grain.tcl" script to visualize these CG bonds as
suggested on the VMD page. I have two different bead types in the system: CA
and CG. In order to visualize the bonds I used the following command line on
Tk console:

source coarse_grained.tcl
g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice}
-color {name name}

After that it gave me the following lines:

[ g_cg ] Processing "topol.tpr"...
[ g_cg ] Create the bond list for 72 atoms...
[ g_cg ] Rebuild bonds...
[ g_cg ] Create representations...

which I understood that all the bonds are created successfully, but when I
looked at the screen  I could see only one of those CG bonds, but not the
others.  Why might be the reason?

Thanks in advance
Ozge Engin
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